It is now widely accepted that mathematical models are needed to predict the behaviour of complex metabolic networks in the cell, in order to have a rational basis for planning metabolic engineering with biotechnological or therapeutical purposes. The great complexity of metabolic networks makes it crucial to simplify them for analysis, but without violating key principles of stoichiometry or thermodynamics. We show here, however, that models for branched complex systems are sometimes obtained that violate the stoichiometry of fluxes at branch points and as a result give unrealistic metabolite concentrations at the steady state. This problem is especially important when models are constructed with the S-system form of biochemical systems theory. However, the same violation of stoichiometry can occur in metabolic control analysis if control coefficients are assumed to be constant when trying to predict the effects of large changes. We derive the appropriate matrix equations to analyse this type of problem systematically and to assess its extent in any given model.